Butternut Squash Mac and Cheese

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Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!

Butternut Squash Mac and Cheese
Butternut Squash Mac and Cheese

A few weeks ago I posted this Cauliflower “Mac” and Cheese recipe that swapped out pasta for cauliflower. Today I bring you this guilt-free mac and cheese recipe. Giving you all the comfort of the classic dish, but with an extra heaping of nutrients.

Butternut Squash Mac and Cheese

Hey there, I’m Heather K. Jones—I’m a dietitian, the nutrition expert for the Skinnytaste cookbooks, and the founder of the weight and wellness program, Feel Better Eat Better. If you struggle with emotional eating or weight anxiety, be sure to check out my free Masterclass by clicking RIGHT HERE. You’ll find out the exact steps I teach my clients to create lasting success from the inside-out, even if they’ve tried everything.

This guilt-free mac and cheese gives you all the comfort of the classic dish, but with an extra heaping of nutrients. Made with whole-wheat noodles, three cheeses (Gruyere, cheddar and Parmesan), shallots, and lots of good-for-your-body butternut squash… it’s cozy, creamy AND nourishing! This is a new staple for me and my sisters. Just add a big green salad and you have the perfect anytime meal.

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Butternut Squash Mac and Cheese
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4.72 from 81 votes
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Butternut Squash Mac & Cheese

275 Cals 13 Protein 43 Carbs 7 Fats
Prep Time: 15 mins
Cook Time: 1 hr
Total Time: 1 hr 15 mins
Yield: 8 servings
COURSE: Brunch, Lunch, Side Dish
CUISINE: American
Butternut Squash Mac and Cheese, a healthier version of macaroni and cheese is so creamy and delicious, no one will ever guess it’s also good for you!


  • Olive oil spray
  • Kosher salt
  • 1 pound cubed butternut squash
  • 10 ounces whole wheat elbow pasta
  • 1 ½ cups low sodium vegetable broth, divided
  • ½ teaspoon onion powder
  • ½ teaspoon garlic powder
  • ¼ cup panko breadcrumbs
  • 2 tablespoons freshly grated Parmesan cheese
  • 1 tablespoon unsalted butter
  • 1 medium shallot, minced
  • ¼ cup all-purpose flour
  • 2 cups skim milk
  • ½ cup shredded gruyere cheese
  • ½ cup shredded cheddar cheese
  • Chopped chives, optional, for garnish


  • Preheat oven to 375 degrees F. Spray a 9” x 11” glass baking dish with oil and set aside.
  • Bring a large pot of salted water to boil. Add squash and boil until tender, 5-6 minutes.
  • When fork tender, transfer squash with a slotted spoon to a blender.
  • Add pasta to boiling water and cook according to package directions. When cooked, drain and put back into the pot.
  • Meanwhile, add ½ cup vegetable broth, onion powder, garlic powder, 1 teaspoon salt and black pepper, to taste to the blender with the squash. Blend until smooth and creamy.
  • In a small bowl, combine breadcrumbs, Parmesan, ¼ teaspoon salt and pepper. Set aside.
  • Melt the butter in a medium sauce pot over medium heat. Add the shallots and sauté 2 minutes. Sprinkle the flour evenly over the shallots and cook another minute.
  • Add the remaining 1 cup broth and milk and whisk to combine. Bring sauce to a boil, then reduce heat to medium-low and cook 5 minutes, whisking frequently.
  • Remove pot from heat and whisk in cheese, pureed squash, 1 1/2 teaspoons salt and pepper.
  • Add sauce to noodles, gently mix to combine, then transfer mixture to prepared baking dish.
  • Sprinkle with breadcrumb mixture and bake 25 minutes. Switch oven to high broil and broil for 2-3 minutes, or until crumbs are starting to brown.



Serving: 1cup, Calories: 275kcal, Carbohydrates: 43g, Protein: 13g, Fat: 7g, Saturated Fat: 4g, Cholesterol: 21mg, Sodium: 462mg, Fiber: 4.5g, Sugar: 5g
WW Points Plus: 8
Keywords: baked mac and cheese, baked macaroni and cheese recipe, butternut mac and cheese, Healthy Macaroni and Cheese

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  1. It’s good in theory but is way too bland. I had to add tarragon, sage, thyme, and basil in it to make it taste like anything. 

  2. This took a little more time to prepare than I normally put into weeknight meals, but WOW! It was worth it! I used Barilla Protein Plus Elbows and Reduced Fat Shredded Cheddar, which lowered the points for me. The only Gruyere I could find in my local market was smoked and that was a yummy plus, in my opinion. I had to be sure to divide this up into servings and store it right away or I would have eaten at least half of it in one sitting! Thanks for yet another great recipe!

  3. I liked this recipe, but, it seemed like a lot of effort. At first, I thought it was too ‘wet’, but, the oven took care of that nicely. Wondering if I can freeze it? 

  4. Can I make and freeze uncooked then bake? Or bake and freeze? Have anyone tried with chickpea noodles? THanks

  5. Love this.  It got my boys to eat some veggies!

  6. Has anyone tried making this with cauliflower instead of noodles? Just wondering about how much cauliflower and if there’s a strategy to keep it from getting too liquidy. 

  7. Loved this except the quantity of salt & pepper in step 9 is off.  Way too much pepper!  

  8. Can you prep it the night before and then cook in the oven the next day? Or would the noodles get too mushy?

  9. If I had puréed my butternut squash prior – how many cups would you suggest to use for the ingredients?

  10. Love this one definitely recommend adding hot sauce at least on top of it. If not just straight in the sauce

  11. Very flavorful! (Almost too salty and I was confused by hos much pepper… but turned out good!) Toddler ate it!

  12. This is the first time in ages I have found a recipe on this site that doesn’t have a button to link to WW personal points. Would it be possible to add one? 

  13. My family loves this recipe, but I feel as if I always have WAY too much sauce.

  14. This is my favorite recipe for a healthy mac and cheese. It has so much flavor! It’s become a staple in my house for sure.
    Thanks for posting this Gina!